The Smallest Biomolecules: Diatomics and their Interactions with Heme Proteins: Diatomics and their Interactions with Heme Proteins
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Table of contents
- Cover
- Table of Contentsv
- Prefaceix
- PART I INTRODUCTORY OVERVIEWS1
- Chapter 1. Mammalian Myoglobin as a Model for Understanding Ligand Affinities and Discrimination in3
- 1. INTRODUCTION3
- 2. LIGAND CONFORMATION AND DISCRIMINATION4
- 3. WATER OR ENDOGENOUS LIGAND DISPLACEMENT5
- 4. LIGAND ENTRY IN THE DISTAL PORTION OF THE HEME CAVITY6
- 5. IRON-LIGAND BOND FORMATION6
- 6. ELECTROSTATIC STABILIZATION OF BOUND LIGANDS7
- 7. FeC–O STRETCHING FREQUENCY, ELECTROSTATIC FIELDS, AND O2 DISSOCIATION RATE CONSTANTS8
- 8. FORMALISM FOR INTERPRETING LIGAND BINDING CONSTANTS9
- 9. REGULATION OF O2 AFFINITY AND LIGAND DISCRIMINATION IN SOYBEAN Lba12
- 10. COMPARISONS BETWEEN ASCARIS SUUM HEMOGLOBIN DOMAIN 1 (AscHb) AND CEREBRATULUS LACTEUS MINI-HEMOG12
- 11. NO BINDING TO FERRIC AND FERROUS HEME PROTEINS14
- 12. SUMMARY14
- ACKNOWLEDGMENTS15
- REFERENCES15
- Chapter 2. A Surfeit of Biological Heme-based Sensors18
- 1. INTRODUCTION18
- 2. WHAT CONSTITUTES A BIOLOGICAL HEME-BASED SENSOR?20
- 3. FAMILIES OF HEME-BASED SENSORS24
- 4. FUTURE DIRECTIONS59
- ACKNOWLEDGMENTS59
- REFERENCES60
- Chapter 3. NO and NOx Interactions with Hemes66
- ABBREVIATIONS66
- 1. INTRODUCTION: REACTIONS OF NO AND NOX IN SOLUTIONS67
- 2. THE FORMATION AND DISSOCIATION OF FERRIC AND FERROUS PORPHYRIN NITROSYL COMPLEXES70
- 3. TRANSFORMATIONS OF COORDINATED NOX75
- 4. REACTIONS OF NO AND NOX WITH HEME MODELS AND PROTEINS IN AQUEOUS MEDIA80
- 5. SUMMARY87
- ACKNOWLEDGMENTS87
- REFERENCES88
- PART II ELECTRONIC STRUCTURE AND SPECTROSCOPY93
- Chapter 4. CO, NO, and O2 as Vibrational Probes of Heme Protein Active Sites95
- ABBREVIATIONS95
- 1. INTRODUCTION96
- 2. FeCO VIBRATIONS98
- 3. Fe(II)NO VIBRATIONS109
- 4. Fe(III)NO VIBRATIONS115
- 5. Fe(II)O2 VIBRATIONS117
- ACKNOWLEDGMENT119
- REFERENCES119
- Chapter 5. Nuclear Resonance Vibrational Spectroscopy „ NRVS124
- ABBREVIATIONS124
- 1. INTRODUCTION124
- 2. EXPERIMENTAL METHODOLOGY126
- 3. APPLICATIONS133
- SUMMARY144
- ACKNOWLEDGMENTS144
- REFERENCES144
- Chapter 6. EPR and Low-temperature MCD Spectroscopy of Ferrous Heme Nitrosyls147
- 1. INTRODUCTION147
- 2. GENERAL CONSIDERATIONS149
- 3. EPR SPECTRA OF FIVE- AND SIX-COORDINATE Fe(II)–PORPHYRIN NO ADDUCTS151
- 4. MCD SPECTROSCOPY ON FERROUS HEME NITROSYLS161
- 5. CONCLUSIONS168
- ACKNOWLEDGMENT168
- REFERENCES168
- PART III ASPECTS OF HEMOGLOBINS (EXCEPT HEME„NOx INTERACTIONS)173
- Chapter 7. Protoglobin and Globin-coupled Sensors175
- 1. BACKGROUND ON THE GLOBINS175
- 2. HISTORY OF THE GLOBIN-COUPLED SENSORS AND THE PROTOGLOBIN176
- 3. GCS FUNCTIONAL CLASSIFICATION176
- 4. BIOPHYSICAL AND KINETIC CHARACTERISTICS190
- 5. MECHANISM OF SIGNALING192
- 6. GCS DIVERSITY AND EVOLUTION194
- 7. PROTOGLOBINS IN THE ARCHAEA196
- 8. ANCIENT OXYGEN SIGNALING AND THE FUTURE199
- ACKNOWLEDGMENTS200
- REFERENCES200
- Chapter 8. Neuroglobin and Cytoglobin203
- 1. GLOBINS: THE ANCIENT PROTEIN SUPERFAMILY CONTAINS TWO NOVICES203
- 2. NEUROGLOBIN: THE DISTANTLY RELATED COUSIN ON OUR NERVESŽ205
- 3. CYTOGLOBIN: MUSCLE MYOGLOBIN’S BROTHER IN FIBROBLASTS AND NEURONS210
- 4. TWO GLOBINS IN SEARCH OF THEIR ROLES IN THE FAMILY (AND IN THE CELL)212
- ACKNOWLEDGMENTS216
- REFERENCES216
- Chapter 9. Extreme pH Sensitivity in the Binding of Oxygen to Some Fish Hemoglobins: The Root Effect219
- 1. BACKGROUND220
- 2. QUANTITATIVE ANALYSIS OF OXYGEN BINDING220
- 3. THE ROOT EFFECT HEMOGLOBINS226
- 4. EVOLUTION AND PHYSIOLOGICAL ROLE OF ROOT EFFECT HEMOGLOBINS226
- 5. MECHANISTIC ORIGINS OF THE ROOT EFFECT227
- 6. STRUCTURAL INTERPRETATIONS OF THE ORIGINS OF THE ROOT EFFECT228
- 7. CONCLUSIONS232
- REFERENCES232
- Chapter 10. Microbial Hemoglobins: Structure, Function, and Folding235
- ABBREVIATIONS235
- 1. HEMOGLOBIN SUPER FAMILY: AN OVERVIEW235
- 2. MICROBIAL HEMOGLOBINS237
- 3. STRUCTURES AND FUNCTIONS OF MICROBIAL HEMOGLOBINS238
- 4. FOLDING STABILITIES OF MICROBIAL Hbs257
- 5. CLOSING REMARKS259
- ACKNOWLEDGMENT261
- REFERENCES261
- PART IV HEME„NOx INTERACTIONS267
- Chapter 11. The Reaction between Nitrite and Hemoglobin: The Role of Nitrite in Hemoglobin-mediated269
- 1. INTRODUCTION269
- 2. THE CHEMISTRY OF THE NITRITE/HEMOGLOBIN REACTION269
- 3. PHYSIOLOGICAL CONSEQUENCES OF THE NITRITE/HEMOGLOBIN REACTION282
- 4. SUMMARY AND CONCLUSIONS286
- ACKNOWLEDGMENTS287
- REFERENCES288
- Chapter 12. Nitric Oxide Dioxygenase: An Ancient Enzymic Function of Hemoglobin290
- 1. Hb FUNCTIONS290
- 2. ROLE FOR Hbs AS NO-METABOLIZING ENZYMES293
- 3. Hb STRUCTURE AND THE NOD MECHANISM300
- 4. EVOLUTION OF Hb FUNCTION313
- 5. INHIBITORS AND APPLICATIONS OF THE NOD REACTION314
- 6. OTHER ENZYMIC FUNCTIONS FOR (FLAVO)Hbs AND Mbs?317
- 7. CONCLUSIONS AND PROSPECTIVE318
- ACKNOWLEDGMENTS319
- REFERENCES319
- Chapter 13. Respiratory Nitric Oxide Reductases, NorB and NorZ, of the Heme–Copper Oxidase Type327
- 1. INTRODUCTION327
- 2. GENETIC ORGANIZATION AND FUNCTIONAL PROPERTIES OF nor GENE PRODUCTS328
- 3. RESPIRATORY NITRIC OXIDE REDUCTASES ARE MEMBERS OF THE HEME–COPPER OXIDASE SUPERFAMILY331
- 4. SHORT-CHAIN RESPIRATORY NITRIC OXIDE REDUCTASE, NorB, IS A COMPLEX WITH CYTOCHROME c335
- 5. THE ACTIVE SITE337
- 6. LONG-CHAIN RESPIRATORY NITRIC OXIDE REDUCTASE, NorZ, IS ALSO A QUINOL OXIDASE343
- 7. STRUCTURAL AND FUNCTIONAL VARIATIONS AMONG RESPIRATORY NITRIC OXIDE REDUCTASES344
- 8. NITRIC OXIDE SIGNALING AND nor GENE REGULATION345
- 9. CONCLUSIONS349
- ACKNOWLEDGMENTS349
- REFERENCES349
- Chapter 14. Nitric Oxide Reductase (P450nor) from Fusarium oxysporum354
- 1. INTRODUCTION354
- 2. ISOLATION OF P450NOR AND MOLECULAR PROPERTIES355
- 3. GENE STRUCTURE OF P450NOR358
- 4. MECHANISTIC STUDIES359
- 5. REACTIONS WITH PEROXYNITRITE363
- 6. CRYSTALLOGRAPHY, X-RAY STRUCTURE, AND ENZYMOLOGY366
- 7. IMPLICATIONS AND OUTLOOK370
- 8. LATEST RESULTS ON THE MOLECULAR MECHANISM OF P450NOR BASED ON COMPUTATIONAL CALCULATIONS372
- ACKNOWLEDGMENTS374
- REFERENCES374
- Chapter 15. Nitric Oxide Interaction with Insect Nitrophorins and Possibilities for the Electron Con378
- 1. BACKGROUND379
- 2. STRATEGIES USED BY BLOOD-SUCKING INSECTS TO INSURE THAT THEY OBTAIN A SUFFICIENT MEAL380
- 3. PROTEIN SEQUENCES AND STRUCTURES OF THE NITROPHORINS FROM R. prolixus.383
- 4. THE SPECIAL PROPERTIES OF NP7387
- 5. NMR SPECTROSCOPIC STUDIES OF THE NITROPHORINS389
- 6. SOURCE OF NO IN THE INSECT SALIVA: A SALIVARY GLAND NO SYNTHASE FROM R. prolixus396
- 7. A NITROPHORIN FROM ANOTHER INSECT: STRUCTURE, SPECTROSCOPIC AND REDOX PROPERTIES OF cNP397
- 8. NITRIC OXIDE REACTIVITY WITH HEME CENTERS403
- 9. REDOX CHEMISTRY OF NO-HEME SYSTEMS INCLUDING THE NITROPHORINS OF R. prolixus404
- 10. POSSIBLE ROLE OF HEME RUFFLING IN STABILIZING THE {FENO}6 CENTER OF THE NITROPHORIN–NO COMPLEX412
- ACKNOWLEDGEMENTS420
- REFERENCES420
- Chapter 16. Bioinorganic Chemistry of the HNO Ligand429
- ABBREVIATIONS429
- 1. NO AND HNO430
- 2. PRODUCTION AND DETECTION OF HNO431
- 3. NITROXYL REVISITED431
- 4. PHYSIOLOGICAL EFFECTS OF FREE NITROXYL433
- 5. THE ENEMAR/FELTHAM BONDING EXTREME435
- 6. BIOLOGICAL ROLES OF NITROXYL INTERMEDIATES436
- 7. NITRITE REDUCTASES436
- 8. NITRIC OXIDE REDUCTASES438
- 9. ELECTROCHEMICAL INVESTIGATIONS440
- 10. NITROXYL ADDUCTS OF HEME PROTEINS444
- 11. BONDING PARAMETERS IN Mb„HNO448
- 12. NON-HEME NITROXYL COMPLEXES451
- 13. SURVEY OF REACTIVITY456
- CONCLUSIONS458
- REFERENCES458
- PART V SELECTED ENZYMES AND SENSORS463
- Chapter 17. Ligand-Protein Interactions in Mammalian Nitric Oxide Synthase465
- ABBREVIATIONS465
- 1. INTRODUCTION466
- 2. SPECTROSCOPIC PROPERTIES OF NOS469
- 3. CARBON MONOXIDE AS A PROBE OF THE CATALYTIC SITE470
- 4. THE NITRIC OXIDE-BOUND COMPLEXES475
- 5. THE EFFECT OF NO ON THE MONOMER/DIMER EQUILIBRIUM481
- 6. OVERVIEW OF NO INTERACTIONS493
- 7. CONCLUSIONS494
- ACKNOWLEDGMENTS495
- REFERENCES495
- Chapter 18. CooA: A Paradigm for Gas-sensing Regulatory Proteins498
- ABBREVIATIONS498
- 1. INTRODUCTION498
- 2. OVERVIEW OF THE SENSING MECHANISMS OF R. rubrum CooA500
- 3. COMPARISON OF R. rubrum CooA STRUCTURE AND EFFECTOR RESPONSE TO THOSE OF CRP503
- 4. HYPOTHESIS FOR ACTIVATION OF CooA BY CO507
- 5. BASIS FOR THE SPECIFICITY FOR CO IN CooA ACTIVATION517
- 6. COOPERATIVITY OF CO BINDING519
- 7. SUMMARY AND FUTURE DIRECTIONS520
- ACKNOWLEDGMENTS521
- REFERENCES521
- Chapter 19. Soluble Guanylyl Cyclase and Its Evolutionary Relatives524
- 1. INTRODUCTION524
- 2. BIOINFORMATIC ANALYSIS OF sGC FAMILY AND GENEALOGY525
- 3. MEASUREMENT OF sGC ACTIVITY AND REGULATION529
- 4. STRUCTURAL HIGHLIGHTS530
- 5. OXYGEN BINDING TO Tt-HNOX533
- 6. REGULATION BY NO, CO, AND OTHER REGULATORY COMPOUNDS534
- 7. OXYGEN-SENSING sGC PROTEINS?535
- 8. FUTURE DIRECTIONS537
- ACKNOWLEDGMENTS537
- REFERENCES537
- Chapter 20. Resonance Raman Studies of the Activation Mechanism of Soluble Guanylate Cyclase540
- 1. INTRODUCTION540
- 2. STRUCTURAL CHARACTERISTICS OF sGC542
- 3. ACTIVATORS OF sGC544
- 4. SPECTROSCOPIC CHARACTERIZATION OF sGC546
- 5. EFFECTS OF SUBSTRATE AND ANALOGUES556
- 6. CHANGES IN HEME VIBRATIONS557
- 7. MECHANISM OF ACTIVATION557
- 8. PROSPECTS560
- REFERENCES561
- Chapter 21. Insights into Heme-based O2 Sensing from Structure–Function Relationships in the FixL564
- ABBREVIATIONS565
- 1. INTRODUCTION566
- 2. FixL PROTEINS567
- 3. EARLY PHYSICAL CHARACTERIZATION OF FixLs AND THEIR HEME LIGAND COMPLEXES569
- 4. STRUCTURAL STUDIES574
- 5. NON-EQUILIBRIUM, LIGAND-COUPLED DYNAMICS AS A PROBE OF SIGNAL TRANSDUCTION580
- 6. ROLE OF FixL ASSOCIATION586
- 7. SITE-DIRECTED MUTAGENESIS STUDIES587
- 8. PERSPECTIVES593
- REFERENCES594
- Index597
This is not a book on NO biology, nor about hemoglobin, nor about heme-based sensors per se. Of course, it covers all these topics and more, but above all, it aims at providing a truly multidisciplinary perspective of heme-diatomic interactions. The overarching goal is to build bridges among disciplines, to bring about a meeting of minds.
The contributors to this book hail from diverse university departments and disciplines – chemistry, biochemistry, molecular biology, microbiology, zoology, physics, medicine and surgery, bringing with them very different views of heme-diatomic interactions. The hope is that the juxtaposition of this diversity will lead to increased exchanges of ideas, approaches, and techniques across traditional disciplinary boundaries.
The authors represent a veritable Who’s Who of heme protein research and include John Olson, Tom Spiro, Walter Zumft, F. Ann Walker, Teizo Kitagawa, W. Robert Scheidt, Pat Farmer, Marie-Alda Gilles-Gonzalez, and many other equally distinguished scientists.
Extremely distinguished list of authors
Multidisciplinary character – equally suitable for chemists and biochemists
Covers the hottest topics in heme protein research: sensors, NO biology, new roles of hemoglobin, etc.
The contributors to this book hail from diverse university departments and disciplines – chemistry, biochemistry, molecular biology, microbiology, zoology, physics, medicine and surgery, bringing with them very different views of heme-diatomic interactions. The hope is that the juxtaposition of this diversity will lead to increased exchanges of ideas, approaches, and techniques across traditional disciplinary boundaries.
The authors represent a veritable Who’s Who of heme protein research and include John Olson, Tom Spiro, Walter Zumft, F. Ann Walker, Teizo Kitagawa, W. Robert Scheidt, Pat Farmer, Marie-Alda Gilles-Gonzalez, and many other equally distinguished scientists.
Extremely distinguished list of authors
Multidisciplinary character – equally suitable for chemists and biochemists
Covers the hottest topics in heme protein research: sensors, NO biology, new roles of hemoglobin, etc.